Skip to main content

Lund University Publications

LUND UNIVERSITY LIBRARIES

Spatial TCR clonality and clonal expansion in the in situ microenvironment of non-small cell lung cancer

Yu, Hui ; Magoulopoulou, Anastasia ; Amini, Rose Marie ; Chatzinikolaou, Maria Paraskevi ; Horie, Masafumi ; Lindberg, Amanda ; Mezheyeuski, Artur ; Backman, Max ; Metousis, Andreas and Brunnström, Hans LU orcid , et al. (2025) In Journal for ImmunoTherapy of Cancer 13(8).
Abstract

Background T-cell activation and clonal expansion are essential to effective immunotherapy responses in non-small cell lung cancer (NSCLC). The distribution of T-cell clones may offer insights into immunogenic mechanisms and imply potential prognostic and predictive information. Methods We analyzed α/β T-cell receptor (TCR) clonality using RNA-sequencing of bulk frozen tumor tissue from 182 patients with NSCLC. The data was integrated with molecular and clinical characteristics, extensive in situ imaging, and spatial sequencing of the tumor immune microenvironment. TCR clonality was also determined in an independent cohort of nine patients with immune checkpoint-treated NSCLC. Results TCR clonality (Gini index) patterns ranged from high... (More)

Background T-cell activation and clonal expansion are essential to effective immunotherapy responses in non-small cell lung cancer (NSCLC). The distribution of T-cell clones may offer insights into immunogenic mechanisms and imply potential prognostic and predictive information. Methods We analyzed α/β T-cell receptor (TCR) clonality using RNA-sequencing of bulk frozen tumor tissue from 182 patients with NSCLC. The data was integrated with molecular and clinical characteristics, extensive in situ imaging, and spatial sequencing of the tumor immune microenvironment. TCR clonality was also determined in an independent cohort of nine patients with immune checkpoint-treated NSCLC. Results TCR clonality (Gini index) patterns ranged from high T-cell clone diversity with high evenness (low Gini index) to clonal dominance with low evenness (high Gini index). Generally, TCR clonality in cancer was lower than in matched normal lung parenchyma distant from the tumor (p=0.021). The TCR clonality distribution between adenocarcinoma and squamous cell carcinoma was similar; however, smokers showed a higher Gini index. While in the operated patient with NSCLC cohort, TCR clonality was not prognostic, in an immune checkpoint inhibitor-treated cohort, high TCR clonality was associated with better therapy response (p=0.016) and prolonged survival (p=0.003, median survival 13.8 vs 2.9 months). On the genomic level, a higher Gini index correlated strongly with a lower frequency of epidermal growth factor receptor (EGFR) and adenomatous polypsis coli (APC) gene mutations, but a higher frequency of P53 mutations, and a higher tumor mutation burden. In-depth characterization of the tumor tissue revealed that high TCR clonality was associated with an activated, inflamed tumor phenotype (PRF1, GZMA, GZMB, INFG) with exhaustion signatures (LAG3, TIGIT, IDO1, PD-1, PD-L1). Correspondingly, PD-1+, CD3+, CD8A+, CD163+, and CD138+immune cells infiltrated cancer tissue with high TCR clonality. In situ sequencing recovered single dominant T-cell clones within the patient tumor tissue, which were predominantly of the CD8 subtype and localized closer to tumor cells.

(Less)
Please use this url to cite or link to this publication:
author
; ; ; ; ; ; ; ; and , et al. (More)
; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; and (Less)
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Clonality, Immune Checkpoint Inhibitor, Lung Cancer, T cell, T cell Receptor - TCR
in
Journal for ImmunoTherapy of Cancer
volume
13
issue
8
article number
e012089
publisher
BMJ Publishing Group
external identifiers
  • pmid:40866291
  • scopus:105014547317
ISSN
2051-1426
DOI
10.1136/jitc-2025-012089
language
English
LU publication?
yes
id
48605dcb-7ed3-46ad-b62b-eebc6a68403d
date added to LUP
2025-10-20 14:29:56
date last changed
2025-10-21 03:00:02
@article{48605dcb-7ed3-46ad-b62b-eebc6a68403d,
  abstract     = {{<p>Background T-cell activation and clonal expansion are essential to effective immunotherapy responses in non-small cell lung cancer (NSCLC). The distribution of T-cell clones may offer insights into immunogenic mechanisms and imply potential prognostic and predictive information. Methods We analyzed α/β T-cell receptor (TCR) clonality using RNA-sequencing of bulk frozen tumor tissue from 182 patients with NSCLC. The data was integrated with molecular and clinical characteristics, extensive in situ imaging, and spatial sequencing of the tumor immune microenvironment. TCR clonality was also determined in an independent cohort of nine patients with immune checkpoint-treated NSCLC. Results TCR clonality (Gini index) patterns ranged from high T-cell clone diversity with high evenness (low Gini index) to clonal dominance with low evenness (high Gini index). Generally, TCR clonality in cancer was lower than in matched normal lung parenchyma distant from the tumor (p=0.021). The TCR clonality distribution between adenocarcinoma and squamous cell carcinoma was similar; however, smokers showed a higher Gini index. While in the operated patient with NSCLC cohort, TCR clonality was not prognostic, in an immune checkpoint inhibitor-treated cohort, high TCR clonality was associated with better therapy response (p=0.016) and prolonged survival (p=0.003, median survival 13.8 vs 2.9 months). On the genomic level, a higher Gini index correlated strongly with a lower frequency of epidermal growth factor receptor (EGFR) and adenomatous polypsis coli (APC) gene mutations, but a higher frequency of P53 mutations, and a higher tumor mutation burden. In-depth characterization of the tumor tissue revealed that high TCR clonality was associated with an activated, inflamed tumor phenotype (PRF1, GZMA, GZMB, INFG) with exhaustion signatures (LAG3, TIGIT, IDO1, PD-1, PD-L1). Correspondingly, PD-1+, CD3+, CD8A+, CD163+, and CD138+immune cells infiltrated cancer tissue with high TCR clonality. In situ sequencing recovered single dominant T-cell clones within the patient tumor tissue, which were predominantly of the CD8 subtype and localized closer to tumor cells.</p>}},
  author       = {{Yu, Hui and Magoulopoulou, Anastasia and Amini, Rose Marie and Chatzinikolaou, Maria Paraskevi and Horie, Masafumi and Lindberg, Amanda and Mezheyeuski, Artur and Backman, Max and Metousis, Andreas and Brunnström, Hans and Marincevic, Millaray and Botling, Johan and Mattsson, Johanna Sofia Margareta and Kärre, Klas and Leandersson, Karin and Nilsson, Mats and Strell, Carina and Micke, Patrick}},
  issn         = {{2051-1426}},
  keywords     = {{Clonality; Immune Checkpoint Inhibitor; Lung Cancer; T cell; T cell Receptor - TCR}},
  language     = {{eng}},
  number       = {{8}},
  publisher    = {{BMJ Publishing Group}},
  series       = {{Journal for ImmunoTherapy of Cancer}},
  title        = {{Spatial TCR clonality and clonal expansion in the in situ microenvironment of non-small cell lung cancer}},
  url          = {{http://dx.doi.org/10.1136/jitc-2025-012089}},
  doi          = {{10.1136/jitc-2025-012089}},
  volume       = {{13}},
  year         = {{2025}},
}